GENOMICA COMPARADA DE BACTERIAS

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GENOMICA COMPARADA DE BACTERIAS

• Alex Mira y Francisco Rodríguez-Valera
• División de Microbiología

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Características generales de los genomas
procarióticos

• Tamaño pequeño 0.5 (Mycoplasma 10 Mb
  Myxococcus), media 2 MB (5 con morfogénesis)
• Densidad codificante alta ca. 90 (no intrones,
  DNA repetido)
• Haploides, no meiosis ni reprod. Sexual
• Genes agrupados (operones, clusters funcionales,
  islas genómicas etc.)
• Diferentes tipos de replicones cromosoma/s,
  plásmidos, fagos, transposones replicativos etc.
• Intrínsecamente plásticos (contenido en genes,
  orden de genes, fusión de replicones etc, etc.

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Genome size (bp)
Taxonomy group
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Características generales de los genomas
procarióticos

• Tamaño pequeño 0.5 (Mycoplasma 10 Mb
  Myxococcus), media 2 MB (5 con morfogénesis)
• Densidad codificante alta ca. 90 (no intrones,
  DNA repetido)
• Haploides, no meiosis ni reprod. Sexual
• Genes agrupados (operones, clusters funcionales,
  islas genómicas etc.)
• Diferentes tipos de replicones cromosoma/s,
  plásmidos, fagos, transposones replicativos etc.
• Intrínsecamente plásticos (contenido en genes,
  orden de genes, fusión de replicones etc, etc.

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Características generales de los genomas
procarióticos

• Tamaño pequeño 0.5 (Mycoplasma 10 Mb
  Myxococcus), media 2 MB (5 con morfogénesis)
• Densidad codificante alta ca. 90 (no intrones,
  DNA repetido)
• Haploides, no meiosis ni reprod. Sexual
• Genes agrupados (operones, clusters funcionales,
  islas genómicas etc.)
• Diferentes tipos de replicones cromosoma/s,
  plásmidos, fagos, transposones replicativos etc.
• Intrínsecamente plásticos (contenido en genes,
  orden de genes, fusión de replicones etc, etc.

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Características generales de los genomas
procarióticos

• Tamaño pequeño 0.5 (Mycoplasma 10 Mb
  Myxococcus), media 2 MB (5 con morfogénesis)
• Densidad codificante alta ca. 90 (no intrones,
  DNA repetido)
• Haploides, no meiosis ni reprod. Sexual
• Genes agrupados (operones, clusters funcionales,
  islas genómicas etc.)
• Diferentes tipos de replicones cromosoma/s,
  plásmidos, fagos, transposones replicativos etc.
• Intrínsecamente plásticos (contenido en genes,
  orden de genes, fusión de replicones etc, etc.

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Características generales de los genomas
procarióticos

• Tamaño pequeño 0.5 (Mycoplasma 10 Mb
  Myxococcus), media 2 MB (5 con morfogénesis)
• Densidad codificante alta ca. 90 (no intrones,
  DNA repetido)
• Haploides, no meiosis ni reprod. Sexual
• Genes agrupados (operones, clusters funcionales,
  islas genómicas etc.)
• Diferentes tipos de replicones cromosoma/s,
  plásmidos, fagos, transposones replicativos etc.
• Intrínsecamente plásticos (contenido en genes,
  orden de genes, fusión de replicones etc, etc.

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The genome of the bacterium Borrelia burgdorferi
B31, the aetiologic agent of Lyme disease,
contains a linear chromosome of 910,725 base
pairs and at least 17 linear and circular
plasmids with a combined size of more
than 533,000 base pairs.
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Bacterial chromosomes sizes
Linear chromosome
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Características generales de los genomas
procarióticos

• Tamaño pequeño 0.5 (Mycoplasma 10 Mb
  Myxococcus), media 2 MB (5 con morfogénesis)
• Densidad codificante alta ca. 90 (no intrones,
  DNA repetido)
• Haploides, no meiosis ni reprod. Sexual
• Genes agrupados (operones, clusters funcionales,
  islas genómicas etc.)
• Diferentes tipos de replicones cromosoma/s,
  plásmidos, fagos, transposones replicativos etc.
• Intrínsecamente plásticos (contenido en genes,
  orden de genes, fusión de replicones etc, etc.

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TRAITS INTRODUCED THOUGH LATERAL GENE TRANSFER
Pathogenicity Islands dictate disease condition
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Comparación genoma K12 (4,6 Mb) con O157 (5,5 Mb)

• 4.1 Mb común backbone
• 1.34 Mb presente en O157 y no K12
• 0.53 Mb presente en K12 y no O157
• En O157 hay 177 islas de más de 50pb, la más
  grande con 106 genes (197 Kb), el 25 de los
  genes están en islas
• 9 islas de más de 15 Kb contienen factores de
  virulencia

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Uropathogenic Escherichia coli
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Non-pathogenic
Uropathogenic
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Total Genes 7638 40 in all three 13 in 2 out
of 2 47 in 1 out of 3
Enterohaemorrhagic
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Human
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Drosophila
70 genes in common
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Molecules as Documents of Evolutionary History
Different types of molecules are discussed in
relation to their fitness for providing the
basis for a molecular phylogeny. Best fit are the
semantides, i.e. the different types of
macromolecules that carry the genetic
Information.
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Ribosome
5S rRNA
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Methanococcus vannielli
Saccharomyces cerevisiae
Escherichia coli
16S rRNA
18S rRNA
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The purple bacteria Proteobacteria
? Neisseria, Burkholderia, Beggiatoa,
Thiobacillus ? Vibrio, Pseudomonas,
enterobacteria
? Desulfovibrio, Bdellovibrio
? Nitrobacter, Rhizobium, Rickettsia, Brucella
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Ribosomal RNA phylogeny and the primary lines of
evolutionary descent
...developments in molecular phylogeny using
ribosomal RNA (rRNA) sequences have revealed the
outlines of the master phylogenetic tree relating
all known life-forms.
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Discover, December 1990 p76
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Classification
Systematics
Taxonomy
Phylogeny
E. coli O157H7 adhered to Hep-2 cells
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Haemophilus influenzae
1,839,137 bp
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Mycoplasma genitalium
580,070 bp
Comparison of this genome to that of Haemophilus
influenzae suggests that differences in genome
content are reflected as profund differences in
physiology and metabolic capacity between these
two organisms
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Circular map of Sf301 chromosome compared with
those of E.coli K12 MG1655 and 0157 EDL933.
The hyperthermophile Thermoanaerobacter
tencongenest 258 of 2588 proteins (10) with
significantly greater similarity to archaeal than
to bacterial homologs.
The mesophile Metanosacrina acetivorans. 1453 of
4540 proteins (32) with sifnificantly greater
similarity to bacterial than to archaeal homologs.
Genomic maps of apparent phylogenetic affinities
for two bacterial genomes.
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TRAITS INTRODUCED THROUGH LATERAL GENE TRANSFER
Antibiotics that have been used as growth
promoter in animal husbandry caused
crossresistance to antibiotics used in human
chemotherapy
Antibiotic resistance
VRE has spread among humans
Vancomycin-resistant enterococci (VRE) Potential
reservoir of transferable vanA mediated
glycopeptide resistance. vanA is a transposon
related to Tn1546
Potential risk to transfer vanA to MRSA
(meticillin resistan S. aureus). Vancomycin is
the antibiotic used to threat this microorganism
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Transfer of antibiotic resistance genes between
Gram positive and Gram negative bacteria
Courvalin P (1994) Antimicrob Agents Chemothe
38 1447?1451
Genes from Gram positive microorganisms are
readily expressed in Gram negative bacteria,
whereas the reverse is generally not true, exerts
a strong directional selection
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Demostrated range of gene transfer
(Amábile-Cuevas CF, Chicurel ME (1992) Cell 70
189?199)
The amount and source of horizontal gene transfer
can be linked to an organisms lifestyle and
phylogeny
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Distribution of horizontaly acquired (foreign)
DNA in some sequenced bacterial genomes
protein-coding sequence (kb)
Nature (2000) 405, 299?304
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Demonstration of horizontal transfer acquisition
of operons Koonin EV, Makarova KS, Aravind L
(2001) Annu Rev Microbiol 55 709?742
It has been determined that the presence of three
or more genes in the same order in distant
genomes is extremely unlikely unless these genes
form an operon. Each operon typically emerges
only once during evolution and is maintained by
selection ever after.
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Horizontal gene transfer
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Horizontal transfer conjugation
Conjugation has the greatest requeriments
element (plasmid or transposon) and donor and
recipient cells must establish a physical contact
sufficiently stable to allow transfer of DNA.
Both cells have to be metabolically active to
allow DNA synthesis and other activities.
Conjugation can mediate the transfer of genetic
material between Domains (e.g., between
bacteria and plants, and between bacteria and
yeast)
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Bacterial conjugation in the environment
Davison J (1999) Plasmid 42 73?91
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Transposons and insertion sequences
Transposition movement of discrete genetic units
(insertion sequences and transposons) from one
location to another, and particularly from one
genome to another. Translocable elements revealed
that genomes are far more plastic than was
previously thought, and provide an
explanation for how plasmids could capture new
genes
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Properties of selected Insertion sequences
Inverted repeat (Length in bp)
Target site (Length in bp)
Number of copies on E. coli chromos.
Insertion sequence
Length (bp)
IS1 768
23 9 or 8
6?10 IS2
1327 41
5 4 ?13
(1)a IS3 1400
38 3 ?4
5 ?6 (2) IS4
1428 18
11 or 12 1
?2 IS5 1195
16 4
10 ?11
aThe value in parenthesis indicates the number of
IS elements on the F factor
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Structure of R plasmids and transposons
The resitance transfer factor (RTF) codes for the
proteins necessary for plasmid replication and
transfer. The structure of Tn3 is shown in more
detail
RTF
IS1
IS1
Cm chloramphenicol Sm, Su streptomycin,
sulfonamide Ap ampicilin km kanamycin
Cm
km
Sm, Su
Ap
Tn4
Tn3
38 bp inverted repeat
38 bp inverted repeat
tnpA
tnpR
Transposase
?-lactamase
Resolvase
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Horizontal transfer Transduction
New genetic material can be introduced into a
bacterium by a bacteriophage that has replicated
within a donor microorganism and packaged random
DNA fragments (generalized transduction) or the
DNA adjacent to the phage attachment (specialized
transduction).
The amount of DNA that can be transferred in a
single event is limited by the size of the phage
capsid, but can range upwards up of 100 kb.
Although phages are prevalent in the environment,
the spectrum of microorganisms that can be
transduced depends upon receptors recognized by
the phage. Transduction does not require donor
and recipient cells to be present at the same
place, or even the same time.
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Certain strains of Corynebacterium diphtheriae
are lysogenized by bacteriophage ?, and thee
strains produce the diphteria toxin, that
inhibits eukarytic (and archaean) protein
synthesis and thus kills cells. The
pseudomembrane that forms in diphteria may block
the passage of air, and death from diphteria is
usually due to a combination of the effects of
suffocation and tissue destruction by exotoxin
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Horizontal transfer Transformation
Transformation involves the uptake of naked DNA
from the environment, it does not require even a
living donor cell because release of DNA during
death and cell lysis provide free DNA. The
persistance and dissemination of DNA in
the environment determine how far in time and
space the recipient cell can be separated from
the donor. The recipient must be physiologically
active to be able to take up DNA.
Effective transformation in N. gonorrhoeae and H.
influenzae requires the presence of specific
recognition sequences (5 ?GCCGTCTGAA ? 3 and 5
?AAGTGCGGT ? 3, respectiv.). Although the
presence of specific uptake sequences enhances
the transformation efficiency between related
species (e.g., H. parainfluenzae to H.
influenzae), many of the naturally competent
bacterial species, such as B. subtilis and S.
pneumoniae, do not display sequence preference
and are capable of high levels of transformation.
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Transformation mechanism
Transformation frequency (log)
Lag phase
Exponential phase
Neisseria spp., H. influenzae are perpetually
competent to accept DNA, whereas B. subtilis and
S. pneumoniae become competent upon reaching a
certain physiological stage in their life cycle
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TRAITS INTRODUCED THOUGH LATERAL GENE TRANSFER
Pathogenicity Islands dictate disease condition
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Demostrated range of gene transfer
(Amábile-Cuevas CF, Chicurel ME (1992) Cell 70
189?199)
The amount and source of horizontal gene transfer
can be linked to an organisms lifestyle and
phylogeny
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Genomas procarióticos

• Alta densidad de codificación (tipic.90, en
  humano 3, en S. cerevisiae 70)
• Alta variabilidad en contenido incluso dentro de
  una especie.
• Genes agrupados en operones, grupos funcionales,
  islas etc.
• Mosaico en términos de GC o uso de codones
• Alta plasticidad incluso dentro de la especie.

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Recombinación aditiva

• El tamaño del genoma de algunas especies
  bacterianas puede variar en 1 Mb según las cepas
• Islas de patogenicidad
• Genomas completos

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Succession of genetic events contributing to
virulence in Shigella
Virulence plasmid
SHI-2
SHI-1
SHI-2
SHI-1
ompT
cadA
Shigella
E. coli ancestor
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